Rigidity Theory-Based Approximation of Vibrational Entropy Changes upon Binding to Biomolecules

We introduce a computationally efficient approximation of vibrational entropy changes (ΔS vib) upon binding to biomolecules based on rigidity theory. From constraint network representations of the binding partners, ΔS vib is estimated from changes in the number of low frequency (“spongy”) modes with...

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Bibliographic Details
Published in:Journal of chemical theory and computation 2017-04, Vol.13 (4), p.1495-1502
Main Authors: Gohlke, Holger, Ben-Shalom, Ido Y, Kopitz, Hannes, Pfeiffer-Marek, Stefania, Baringhaus, Karl-Heinz
Format: Article
Language:English
Subjects:
Binding Sites
Entropy
Proteins - chemistry
Quantum Theory
Small Molecule Libraries - chemistry
Vibration
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Summary:We introduce a computationally efficient approximation of vibrational entropy changes (ΔS vib) upon binding to biomolecules based on rigidity theory. From constraint network representations of the binding partners, ΔS vib is estimated from changes in the number of low frequency (“spongy”) modes with respect to changes in the networks’ coordination number. Compared to ΔS vib computed by normal-mode analysis (NMA), our approach yields significant and good to fair correlations for data sets of protein–protein and protein–ligand complexes. Our approach could be a valuable alternative to NMA-based ΔS vib computation in end-point (free) energy methods.
ISSN:1549-9618
1549-9626
DOI:10.1021/acs.jctc.7b00014